[gmx-users] Question about adding hydrogens to a newly constructed residue
Mark Abraham
Mark.Abraham at anu.edu.au
Tue Sep 6 02:52:46 CEST 2011
On 6/09/2011 1:44 AM, J. Nathan Scott wrote:
>
>
> On Mon, Sep 5, 2011 at 9:29 AM, Mark Abraham <Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
>
> On 6/09/2011 1:22 AM, J. Nathan Scott wrote:
>>
>>
>> On Sun, Sep 4, 2011 at 11:51 AM, Mark Abraham
>> <Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>> wrote:
>>
>> On 5/09/2011 3:30 AM, J. Nathan Scott wrote:
>>
>> Hello fellow GROMACS users,
>>
>> I am in the process of constructing a new residue in the
>> OPLS-AA force field for the mCherry chromophore. However,
>> I am having some difficulty in adding three CH3
>> hydrogens. In the 2H5Q PDB structure the chromophore
>> residue, CH6, has CE1 and CE2 ring carbons defined, but
>> also an extended chain carbon named CE. The problem is
>> that my hdb rules were assigning HE1 and HE2 to the ring
>> carbon hydrogens (1 1 HE1 CE1 CD1
>> CZ for example), and HE1, HE2, and HE3 to the CE carbon
>> hydrogens (3 4 HE CE SD CG1).
>> Since these hydrogens are of different types, I need to
>> have them named distinctly in my RTP file and need for
>> Gromacs to understand them as different types. I changed
>> the CH6 residue's CE atom to CE3 in the PDB file and the
>> relevant RTP entries accordingly (see below). I also
>> changed the hdb entry for the new CE3 atom (also below).
>>
>> Relevant RTP lines:
>> CE3 opls_209 0.0 10
>> HE31 opls_140 0.0 11
>> HE32 opls_140 0.0 12
>> HE33 opls_140 0.0 13
>> CE1 opls_145 0.0 32
>> HE1 opls_146 0.0 33
>> CE2 opls_145 0.0 34
>> HE2 opls_146 0.0 35
>> [bonds]
>> CE3 HE31
>> CE3 HE32
>> CE3 HE33
>> CE1 HE1
>> CE2 HE2
>>
>> Relevant HDB lines:
>> 3 4 HE3 CE3 SD CG1
>> 1 1 HE1 CE1 CD1 CZ
>> 1 1 HE2 CE2 CD2 CZ
>>
>> I thought this would cover everything, but I am receiving
>> the following sort of error from pdb2gmx for each of the
>> the three CE3 hydrogens(pdb2gmx -f 2H5Q.pdb -o
>> 2H5Q_processed.gro -water tip3):
>>
>> "WARNING: atom HE31 is missing in residue CH6 66 in the
>> pdb file
>> You might need to add atom HE31 to the hydrogen
>> database of building block CH6
>> in the file aminoacids.hdb (see the manual)"
>>
>> I've looked at other examples in the aminoacids.hdb file
>> and cannot figure out what I am missing here, it seems
>> like my hdb rule should be adding 3 type 4 hydrogens
>> named HE31, HE32, and HE33. I am assuming that the other
>> hdb rules are OK, since they seemed to work fine before,
>> as indicated by examining the gro file. I would sincerely
>> appreciate any help you can offer. Thank you!
>>
>>
>> I can't see a reason why that wouldn't work. However, there's
>> no need for you to preserve the PDB atom name for CE.
>> Reducing the potential for some atom-naming screw-up such as
>> this is a good reason to change it (in both your coordinate
>> file and .rtp entry). It will probably just work, or at the
>> very least simplify further trouble-shooting.
>>
>> Mark
>>
>>
>> Hello Mark, thank you for your help, but I took your very
>> reasonable advice and am still receiving the exact same sort of
>> error. I changed the PDB file atom name to CQ, which of course
>> makes it unique within that residue (and indeed in the whole PDB
>> file). I updated my .rtp entries and the .hdb rules accordingly,
>> and yet I still receive the exact same sort of error. It seems as
>> if something is wrong with my hdb syntax, but having looked at
>> numerous other examples in the hdb file and online I am at a loss
>> as to what the problem might be. For what it's worth, if I use
>> the -missing switch when I run pdb2gmx, the other CH6 hydrogen
>> atoms appear to be added correctly in the resulting gro file,
>> with the names exactly as I expected from the hdb naming rules.
>>
>>
>> My input:
>> pdb2gmx -f 2H5Q_spdbv.pdb -o 2H5Q_processed.gro -water tip3
>>
>> Error received:
>> "WARNING: atom HQ1 is missing in residue CH6 66 in the pdb file
>> You might need to add atom HQ1 to the hydrogen database
>> of building block CH6
>> in the file aminoacids.hdb (see the manual)"
>>
>> "WARNING: atom HQ2 is missing in residue CH6 66 in the pdb file
>> You might need to add atom HQ1 to the hydrogen database
>> of building block CH6
>> in the file aminoacids.hdb (see the manual)"
>>
>> "WARNING: atom HQ3 is missing in residue CH6 66 in the pdb file
>> You might need to add atom HQ1 to the hydrogen database
>> of building block CH6
>> in the file aminoacids.hdb (see the manual)"
>>
>>
>>
>> PDB file:
>> ATOM 493 CQ CH6 A 66 42.848 20.230 6.798 1.00 40.19
>>
>> hdb file:
>> CH6 9
>> 2 6 HG1 CG1 SD CB1
>> 2 6 HB1 CB1 CG1 CA1
>> 2 6 HA3 CA3 C3 N3
>> 1 1 HB2 CB2 CA2 CG2
>> 1 1 HD1 CD1 CE1 CG2
>> 1 1 HD2 CD2 CE2 CG2
>> 1 1 HE1 CE1 CD1 CZ
>> 1 1 HE2 CE2 CD2 CZ
>> 3 4 HQ CQ SD CG1
>>
>> rtp file (relevant portions only):
>> CQ opls_209 0.0 10
>> HQ1 opls_140 0.0 11
>> HQ2 opls_140 0.0 12
>> HQ3 opls_140 0.0 13
>> [bonds]
>> SD CQ
>> CQ HQ1
>> CQ HQ2
>> CQ HQ3
>>
>> I forgot to mention before, my GMX version is 4.5.4, running on a
>> RHEL6 workstation. Thank you sincerely for any troubleshooting
>> assistance you can provide. I am quite stumped by this problem!
>
> Weird. Does naming the residue something other than CH6 help?
> Specifically, something all letters. Has that residue been added
> as Protein to the residuetypes.dat? General advice here:
> http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
>
> Mark
>
>
> Aha! That did the trick! I changed the residue name to CHB in the
> input PDB file, the hdb file, the rtp file, and residuetypes.dat (I
> did have CH6 defined there as protein, by the way), and now pdb2gmx is
> adding those three hydrogens with no problem whatsoever. Thank you
> again very much, it never occurred to me that the residue name could
> be an issue.
>
> I think I'll file a bug report on this. If nothing else this behavior
> is certainly unexpected, since pdb2gmx never mentions any possible
> issues with a number in the residue name.
Yes, please do that on the GROMACS Redmine. Please provide a tarball of
a set of files that can reproduce the issue.
Mark
>
> Thank you again very much for your help with this!
>
> -Nathan
>
>
> --
> ----------
> J. Nathan Scott, Ph.D.
> Postdoctoral Fellow
> Department of Chemistry and Biochemistry
> Montana State University
>
>
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